Baseline
by secondhandsaint
Summary: Two years after obtaining Alphonse's body, Edward must now find a way to keep it. With only ten months and the Truth's own set of rules, he has to find a way to pay the price. Or they could both lose everything. T to be safe.
1. Prologue

Title: Baseline  
>Author: secondhandsaint<br>A/N: This story mixes ideas from both the manga and the original anime, though follows much more closely the latter. It disregards the movie as well as the portion of the plot involving Gate travel. This is an alternate to the end of the series.

* * *

><p><strong>Baseline<strong>

**secondhandsaint**

**Prologue**

The scent of electricity hung heavy in the air and stung his nose, the charge tingling across his skin and making the hairs on his neck stand on end. The lump in his throat was impossible to move when his throat was so dry and he flinched at the sting when he tried to swallow. It would have suited him better to feel the ground beneath his back, but all he felt was more electricity and the lack of a solid surface concerned him. Frowning, he pulled his heavy eyelids up and was met with white.

A familiar fear filled him and he frowned, heart sinking as he gazed at the great expanse of glowing nothing. He waited for some sort of sign, for the double set of stone doors to appear, for that all-knowing and always hungry form to appear to him.

Clenching his fists, he slowly sat up, motion surprisingly easy considering he was moving in a vacuum, and looked down at himself. He at least had the privilege of keeping his clothes on this time and he frowned once more to see that no one or nothing had come to greet him yet. This was so unlike the other times he'd been here, and it started to scare him slightly. Had he died again? The last time he had been forced into this place flashed through his mind and an ache in his chest caused his hand to raise pressed into the space just below his sternum. Nothing had greeted him then, either.

The thought weighs heavy on him and he sighs as he thinks of his dear little brother pressing his hands to the circle, him standing in the middle with the promise of being whole once again.

"You're not dead, Alchemist."

He whirls around, braid slapping him in the face at the force of it and his eyes narrow at the sight of the presence kneeling before him. The white creature, not human despite its shape, tilts its 'head' as it peers at him and he feels completely and frighteningly exposed. Taking a steadying breath, he clenches his jaw as the creature speaks again.

"You haven't learned a thing since your last visit, have you, Alchemist?"

He didn't know what the creature was talking about. The theory was sound, the circle was perfect. Everything about the transmutation had been calculated and recalculated and recalculated again for good measure. Equivalent exchange was down to the last microgram of matter and he himself had checked the purity of the elements.

"I don't know what you're talking about, Truth! Everything I needed to get my arm and leg back is here, it's a perfect equivalent exchange!"

The creature, Truth, tilts its head the other way this time and he feels like he has just become the punch line of a particularly bad joke. It made him uneasy and he shifts his weight from one foot to another as he waits. For a moment he doesn't think that he will get an elaboration when the creature in front of him stands straight and grins.

"I was referring to your brother."

This startles him and he gulps as the creature moves closer, the electric charge in the air becoming increasingly intense until he can feel the current dancing along his skin. It sets his teeth on edge and he fights the urge to step back.

"Your brother used the Philosopher's Stone within himself to bring you back from the dead, then you sacrificed yourself to do the same for him. Yet you both survived. Where is the equivalent exchange in that?"

Realization dawned on him. He had questioned since the day two years ago that he and his brother had been pulled from the lost city if they had succeeded in cheating Truth. After all, Truth was right: There was absolutely no equivalent exchange in them both being alive. To obtain, something of equal value must be lost.

The creature had begun to circle him, scanning him up and down, probably summing up what the price could be for another visit into Truth.

"And here you are, bartering once again for more when you of all are least deserving."

Now he understood. Truth had been biding its time, waiting until he would do something as foolish as attempt to restore himself back to flesh and bone. He should have never stepped into the circle.

"So greedy, Alchemist!"

The creature tisked in disapproval and reached out, nudging his back and stroking his shoulder, sending shocks across his nerves. Wincing, he stood as still as he could, not wanting to anger the one omniscient power that he believed in, that could take everything from him in an instant. Heart racing, the thought caused him to feel nauseous and he resented being taunted like this. The creature stopped and pulled the tie from his hair, letting golden locks fall loosely around his shoulders in waves and running glowing white fingers through the strands. The action puzzled him.

"Very pretty. Did you know, Alchemist that blonde hair is as close to a genetic baseline as the human race can get? "

Frustrated at the slow torment and the jump from one subject to another, he grit his teeth and glared at the creature before him. The thought that this thing would take his only remaining family from him made his blood boil.

"What do you want for my brother? What do I have to pay?"

The creature appeared to not have heard him and continued to run fingers through his hair, catching a knot occasionally and causing more shocks to shake his body when the creature's skin brushed his. Rather than addressing his question, it continued on.

"Anything less than blond would be pure white, which is the absence of pigment and requires a lack of genetic coding. And females, they're a genetic baseline too. Without it, the human race would have died out eons ago!"

He didn't understand why the Truth was telling him all this when he truly couldn't bring himself to care at the moment. Growling, he fought to keep himself from screaming at the creature, balling his fists so tight his nails threatened to break the skin.

"What do I have to pay? Dammit, what do you want me to give!"

The creature's hands stilled in his hair and for a moment he thought he had pushed too far. Then he felt the fingers unwind themselves from the strands and he was met with the creature face to face, all joking and torment aside.

"Fair trade. I will give you back your limbs and the tools you will need. In return, you will have ten months to repay the full price of your brother's life, given the provided conditions of course."

Golden eyes widened at the timeline and he shook his head. How could he do in ten months what had previously taken them five years to accomplish, and only then by sheer luck? It was an insane thing to ask coming from a supposedly always fair entity.

"Ten months is too short a time!"

Truth stepped back from him, turning and walking away as though suddenly disinterested in him. Scared that he would lose everything if the Truth couldn't be bothered, he stepped forward.

"Please, can't you give me just a little more time?"

The creature stopped and turned back to him, hands folded behind its back. The way it examined him made him gulp down his next breath of air.

"Ten months is plenty of time for what I have planned for you."

Shifting nervously on the spot, he weighed his options. The Truth was practically guaranteeing that he would be able to pay the price for his brother's life, and be given back his limbs. All he had to do was follow a few simple conditions. He couldn't help but feel there was a catch. But as his brother's face flashed through his mind's eye, he knew that if there was a price to be paid, he would gladly pay it for him. Frowning and bracing himself, he lifted his eyes to the creature.

"What conditions?"

The creature slowly began to grin and he felt his fear was confirmed. It was for his brother, he could do this, it was for his brother. Clenching his jaw, he watched as the creature drew closer, reaching out to cup his cheek.

"I've always wanted a baseline…"

He narrowed his eyes, not sure what to make of this and he shuddered at the way the Truth's eyes scanned down him. Drawing a breath, he was about to ask when the creature had disappeared and he was once again faced with the double set of doors, their all-seeing eye fixed on him. His heart dropped into his stomach and his body became cold.

"No…"

The doors swung open and he turned to run. Sticky hands caught him around the middle before he could make it far and he was dragged back towards the doors. Rather than the pain that he had become so accustomed to, he felt stifling heat surround his body as the hands slipped under his clothes.

"No! What are you doing! Stop-"

His words were cut off as one of the hands forced its way into his mouth, sliding down his throat and nearly choking him. Tears sprang to his eyes as he fought for air and tried to move in the heat surrounding him. He felt as though he was melting and being pushed back together. The sensation was oddly similar to what he felt when he was transmuting, only as though every time he had transmuted was compounded on top of each other into him. He struggled for breath and finally the hand in his throat released its grasp, pulling away and making him cough.

His screams burned and seemed to break and pitch. Hands tugged at his hair, his eyes, his waist, chest, legs, groin. With a sizzling pop, he felt the automail be removed from his leg and arm, only to be replaced with flesh, new and feeling.

"Alchemist, why do you fight? You're getting what you came for!"

The Truth's voice made him start and blink his eyes open, kicking against the hands that held him and gasping for air in the suffocating heat. He felt as though he were swimming in it, sinking, unable to catch his breath and he wonders if that was the Truth's intention? To trick him into paying the fare with his life?

All at once he hits the ground with a thud and a whimper, weak and sore. His first thought was to question what the Truth had taken, when the figure stepped in front of him. Moaning, he pushed himself up onto his hands.

His flesh hands, and it is only when he sees this that he notices something else. The fingers are longer, the bones more slender and the skin tone creamy white instead of tanned bronze. He glances up at the Truth to see it is grinning back at him and he shivers. Sitting back on his haunches, he turns his hands over in front of him, shaking as he stares down at himself.

His clothes are loose on his body, pants hanging low on his slim hips despite the belt keeping them up. His legs are still muscular, though thinner than their original shape and his boots feel two sizes too big. His shirt is hanging off of him like a rag, gaping in the front and when he puts his palms against his chest he feels swollen, aching and he flinches. His hair falls into his view, inches longer and blond yet so light it appears a soft baby yellow, wavy down his back.

"Yes, you're still alive."

The voice makes him look up to where the creature had been standing, only to find a reflection of a person in his clothes but could not be him… Could it? Slender, white arms and thing legs, just like the ones he felt. Long wavy blond hair and clothes far too big, just like his own. He raised his hand up to a high cheekbone and the reflection did the same. Golden doe eyes blinked back at him from under long lashes and when he gulped, full pink lips twitched.

"Remember Alchemist: You have ten months to repay the price of your brother's life."

Pulling his eyes away from the reflection of himself –herself?- in such a delicate body, he found himself staring into the eyes of the Truth. Lost for words, he could only stare as the creature grinned.

"If you fail, you and your brother are mine."

Everything went dark and Edward Elric felt herself be pulled into abyss.

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><p>As you can probably guess, this involves gender bending with plot. Before you write it off as a no-go, please at least stick around for the first chapter. Thanks.<p>

SS


	2. 1: Delirium

_baseline (beys-lahyn) – 1. a basic standard or level; guideline. 2. a specific value to establish control in future studies. _

**Baseline**

**secondhandsaint**

**1: Delirium**

Edward swore that if he caught hold of whoever had caused him this pain, he would rip them limb from limb. The first thing he acknowledged while drifting back to consciousness was the pain that spread along his body. The second was that despite sensing he'd been asleep for quite a while, he felt immensely tired. It was as though he had been beaten within an inch of his life and he struggled to come up with an explanation as to why he hurt so badly. He remembered standing in his dorm room, smiling down at Al and then nothing. It confused him and he wondered where he was, if someone knew he was missing and if Al was alright.

Al in danger was a sobering thought and he fought his way further to consciousness. Pain increased tenfold and his body began to sense its true condition. He wasn't quite sure if he had been badly bruised or if many of the bones in his body had been broken. His fingers and toes were numb and he had trouble moving. His breathing was soft and lagging, but it was steady and it took him a moment to realize that it was because he himself was not in control of it, tongue thick around the tube in his throat. The tube was connected to something nearby that let out whooshing noises that went in time to the rise of his chest. He thought he heard muffled voices and was sure he could make out a steady rhythm of beeping.

Concentrating on the beeping, Edward fought the dizzying pain and the fatigued sensation that deadened his body, pulling his eyes open and blinking at the industrial light that flooded his sore eyes. Upon waking the beeping noise grew faster and more insistent, and after a few seconds a new alarm went off, making Edward's head pound. The pain caused him to inhale on his own sharply and soon he found he was choking on the tube in his throat.

Eyes shooting open, he fought to move his numb hands, struggling to grasp the tube with weak fingers. The tube continued to push oxygen into his lungs, but panicking as he was, it wasn't enough. Pain began to push into the back of his mind as his body starved for air and tears streaked down his cheeks. The alarm grew ever more insistent and finally footsteps alerted him to others in the room. A man in a white coat and mint scrubs and a nurse in blue loomed over his bed, and for the first time Edward realized he was in a hospital.

"Shh, it's okay, you need to calm down. The tube is to help you breathe."

He didn't really care at this point, he could breathe on his own if they would just take it out! Gripping the end he gave a swift tug and gagged as the tube refused to budge. Shaking his head, the man turned to the nurse and ordered something. Dizzy from his panic, Edward tried to tug again and the man pulled his hand away and down to his side. Clipping a syringe into the tube, the man pulled the plunger and gripped the tube's end.

"When I say, cough. One, two, three, cough!"

Edward did as instructed and felt the tube scrape along its way up as it was ripped from his throat. He continued to cough and felt as though he would vomit, gasping for breath as nasal cannula tubes were pulled up and around his face, more oxygen tickling his nose. The doctor threw the slimy tracheal tube onto a nearby tray and pulled off his gloves, reaching into his pocket and pulling out a pen.

"I'm Dr. Crenshaw, this is Nurse Taggard. You're in Central General Hospital."

He scanned the doctor up and down, noting his balding brown hair and his glasses sliding down his nose. The nurse was maybe thirty with black hair tucked up in a ponytail. The room itself was cluttered with machines and tubes, a good majority of them attached to him. After a few moments of wheezing, he glanced past the machines, noting the empty bed next to his and feeling his fear rise once more.

"Where's Al?"

His voice sounded like a high croak and it hurt to speak. He was shushed and told not to talk, that it would take a while for his voice to come back. He gripped his throat with his right hand, frowning at the feel. Glancing down at the appendage, he barely registered that it was flesh and bone before his panicked doubled. If he had succeeded in getting his limbs back, where was Al?

"Al? Where's Al? Where's my brother?"

The doctor and nurse glanced between each other and back down at him. The nurse reached forward and brushed her fingers through his bangs, pushing them back and putting on a sympathetic voice.

"No one's here, sweetheart. No one by that name is in this ward."

'Sweetheart?' Sure, he passed for young with his height, but at eighteen he still had matured past 'sweetheart.' Ignoring the nurse patting his head, he turned to the doctor, blinking as he wrote on his chart and glanced at the monitors that recorded his every vital sign. Swallowing past his swollen throat, he tried again.

"Please. He must be nearby. His name is Alphonse Elric. He's seventeen, a little taller than I am, sandy blond hair, hazel eyes…"

He gulped, wincing at the high sound of his voice. Did everyone sound like this after having that tube pulled from their throat? The nurse abandoned her efforts at playing with his hair and poured him a cup of water. Edward took it and drank it down quickly, thankful for the ease it brought to his throat. The nurse thought a moment before shaking her head, hands on her hips.

"Nope, no one registered by that name or description. You were alone when you were found. He's probably at home."

That made him panic again. They didn't have a home. He had seen Al with him before he woke up here and he struggled to remember what had happened before he blacked out. He remembered a circle. He remembered stepping into that circle and Al pressing his hands to it. They were trying to get his limbs back. He closed his eyes and clenched his right hand as he thought of what could possibly have happened to Al.

"Is that your last name, sweetheart? 'Elric?'"

Annoyed at once again being called sweetheart, he nodded his head, looking up to the doctor with desperation in his eyes. He needed to find his brother, now!

"Yes, Elric. Edward Elric. Can you call Central Head Quarters, please? He might be there."

The nurse snickered and played with his hair again and the doctor looked up from the chart. Glancing between the two, Ed couldn't help but feel annoyed that these two refused to pick up the phone and make a damn phone call! He was about to ignore the ache in his body and jump out of bed to do it himself when the nurse's comment made him freeze.

"'Edward?' That's an unusual name."

He blinked and looked back at her. It was no more unusual than John or Eric or Leo, so what gives? Glaring at her, he felt his teeth grind and his fists clench at the blankets of his bed. Behind him, he heard the doctor elaborate for her.

"For a girl, she means. Is it short for something?"

Edward blinked and turned back to him. What did he mean for a girl? Trying to ignore the stinging insult to his manhood, he guessed that these people obviously had never seen a young man with long blond hair before. He didn't have time for this; he needed to find his little brother! Finally fed up and getting nowhere with these people, Edward sat up and pushed the blankets off of himself. Pulling the nasal cannulas off and the pulse oximeter off his finger, he stood. Dizziness threatened to pull him back to the bed and he threw his hands out for balance. The doctor grabbed his arm and Edward winced at the grip.

"Sweetheart, you need to be back in bed."

"Stop calling me sweetheart!"

Edward winced at the shrill sound of his own voice and pulled his arm away from the doctor. Glancing around, he noticed a small phone on a table next to the door to the en suite washroom. Taking a step forward, he gasped when he was caught around the middle, lifted off his feet and pulled back towards his bed.

Instinct took over and he screamed, pounding his fists into the doctor's arms and kicked out. The nurse backed away and he arched his back to try and free himself from the grip. One of his kicks landed against the doctor's knee and he heard a grunt of pain before he was dropped. Landing roughly on the ground, Edward pushed himself off the linoleum and made a break for it again.

"Stop her! Someone grab her!"

Why did they keep confusing him for a girl? He was almost to the phone when a hand wrapped its way around his wrist and swung him around. Distantly he heard the sounds of many people running down the hall and knew that it would soon be at least five against one. Growling, he punched at the doctor, screaming as many big, capable looking orderlies and a few more nurses filled the room.

"Please, I need to find my brother! Let me call someone to find him, please! Let me go, dammit!"

The doctor held tight and drew Edward closer to him, wrapping his arm around his waist and dragging him towards a wall, shouting over Edward's screams.

"She's altered, keeps referring to herself as male. Says her name's Edward. Someone grab her, let's get her in soft restraints."

The moment restraints registered in his mind, Edward flew back into fight mode. Arching hid back, he gave one last hard kick, missing the orderly by a few inches and sending the bathroom door crashing into the wall. The orderly backed away for fear of being kicked and gave Edward a clear view of the mirror on the bathroom wall. What he saw there made him freeze.

A delicate looking girl was hanging in the grip of the doctor he had been fighting, fine-boned and flushed from exertion. Soft yellow hair, lighter than Winry's, fell in wild waves down to a slender waist, hidden slightly by the gaping hospital gown. There is the tiniest hint of a bust and a slender neck. Creamy white skin smoothed over powerful looking legs, thighs muscular and exposed as the hem rode up from struggling. Pink lips parted as their owner gasped for breath and smooth skin complimented an impish face. The only thing that Edward recognized of himself was the golden eyes and even they seemed wrong.

The wind had been knocked out of him and he shook his head in disbelief, the reflection mirroring the action. He suddenly sees a flash of this person in his clothes surrounded by the white inside the Gate. He feels sick and chokes out in a feminine tenor.

"That's not me."

The orderly moves in again and grabs at his legs, the slender legs he had seen in the mirror and he bursts into tears as he struggles to get himself free of their hands. He is choking and panicking and feeling as though there is no way he could trust this body, the body he was trapped in, but he continues to fight as he screams.

"That's not me! My name is Edward Elric, the Fullmetal Alchemist! I'm male, eighteen years old. I have a little brother named Alphonse who's seventeen. My mom's name was Trisha, my dad's Hoenheim of Light. I was born in Resembool on the Eastern Amestris border. I live in CHQ dorm room 306!"

As he shouted whatever information he could think of about himself, Edward turned to various people hoping they would listen to him, hoping something about what he was saying would click. As he turned back to the doctor who had started all this, he saw the man staring back at him with wide eyes and a stunned look. Edward thought he might have him when the doctor collected himself and shouted out his orders.

"Draw up 2mg Ativan!"

"Not Haldol?"

"No, just Ativan!"

One of the nurses made their way to the meds cart in the corner and when she turned, Edward fought against the grip holding him down, anything to keep her from drugging him.

"No, please!"

Kicking and screaming, fighting just to loosen their grip on his limbs, Edward arched his back and twisted his body. Given that it was him against many, he was easily picked up and placed on onto the bed. He felt the sting of an IV being placed at the crook of his elbow and cried out in fear of being drugged. At the sight of the needle, he resorted to begging, trying to get away and crying as the dose was drawn.

"Please! I'm not crazy! Please! Call Roy Mustang! Call him, he's the Flame Alchemist, he's my superior! He's at CHQ, he'll straighten this out. Please call him!"

The needle pushed into the port, the plunger pressed and he felt the antianxiety agent flood into his veins. For a few moments it felt like nothing had happened, then all at once he felt his body start to relax. He let out one more scream before the drug began to take effect, muscles weakening and he sobbed. The room spun slightly as his movements became more uncoordinated and tears streaked his face as his fighting stopped. He could feel the orderlies strap his wrists and ankles into restraints and he continued to cry silently as they left and the nurses took over, replacing the nasal cannulas and pulse oximeter.

While the world dulled as the drugs worked in his system, Edward thought back on what had happened between the time he'd last seen Al to the time he'd woken up here. The memory of sitting in the Gate, staring at this foreign face he was wearing came flooding back and as he fought to keep his eyes open, so did the Truth's words.

"_I've always wanted a baseline…"_

Edward gave a soft sob and let his head roll to the side, staring down at his now flesh right hand, slender and feminine with long fingers and fine bones. He remembered now. The Truth had been angry that both he and Al had bypassed equivalent exchange. He wanted to get even. He wanted a fair trade and to be given what it was owed in the transaction for his little brother's body.

"_You have ten months to repay the price of your brother's life."_

Edward's breathing slowed as the drug pulled him under and he closed his eyes, Truth's words ringing in his ears as he spiralled into unconsciousness.

"_If you fail, you and your brother are mine."_

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><p>Dr. Crenshaw stepped out of room 15, wincing at the throb in his now very sore knee. Pushing his glasses back up his nose, he threw the chart of his Jane Doe down on the nurses' station desk and rubbed eyes, suddenly exhausted.<p>

"_That's not me! My name is Edward Elric, the Fullmetal Alchemist…"_

Knitting his brow, Dr. Crenshaw frowned and flipped open the chart. Taking note of the time on the wall, he wrote down his med orders and glanced at the patient history. Something about this girl just did not seem right. Maybe it was her genuine response to her reflection, or the way she insisted her identity. It tickled something in the back of his mind.

He was about to shrug it off and go down to the cafeteria for a coffee when Nurse Taggard walked out with a personal items bag and a pair of combat boots, plunking them down on the desk and pulling out a Sharpie. Craning his neck to see the contents, he noted with slight interest the very masculine looking clothes, right down to the boxers.

"That our Jane Doe's?"

Nurse Taggard nodded and capped the pen, lifting the bag up and opening the mouth of it wider to shove the boots inside. Dr. Crenshaw was about to turn when the glint of metal caught his eyes and he looked back into the bag, jaw going slack at the small timepiece tucked into the leather pants pocket. Reaching in and grabbing the watch, he stared at the presidential crest imprinted across the plate covering the face of the pocket watch, Nurse Taggard's eyebrow raised.

"Something I can do for you, Dr.?'

For a beat Dr. Crenshaw didn't seem to acknowledge her, then he startled out of his reverie and glanced back up at her, smoothing his thumb over the crest and nodding his head.

"Yeah. You can get me Roy Mustang on the line."

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><p>Okay. Seeing as I got the prologue and the first chapter out in one day, I probably won't get the next chapter out until about Friday. Sorry, but I've got school. For information about medical equipment or vitals, there's google.<p>

SS


	3. 2: Identity

_baseline (beys-lahyn) – 1. a basic standard or level; guideline. 2. a specific value to establish control in future studies. _

**Baseline**

**secondhandsaint**

**2: Identity**

Colonel Roy Mustang pulled into the parking lot just outside of Central General, glancing at the building through the windshield with a feeling of foreboding. Today was not going to go well. Tapping his fingers on the steering wheel, he sighed before looking over at the young man in the passenger's seat. Alphonse Elric turned in kind, unsure of how to go about preparing himself. When his brother's commanding officer had been given the order to 'get his butt down here, ASAP,' he'd practically jumped out of his skin to get to HQ. After waiting for three days for some sort of sign from Edward, a hospital calling was not the cheeriest news they could hope for. Giving a small smile to the sandy-blond, Roy unclipped his seatbelt and opened the car door, stepping out and leading the young man up the steps to the entrance of the hospital.

It took a few moments of paperwork and waiting for the physician in charge of Edward's case, but as the doctor approached with a thick looking chart and a tired look, Roy steeled himself for the worst. He'd been told to come to the hospital to identify someone that may be Edward; he just hoped it wouldn't be in a morgue. The doctor nodded his head in greeting and held out his hand.

"I'm Crenshaw, we spoke on the phone."

Roy took the man's hand and gave it a firm shake, thankful for something for his own to do to keep it from trembling. The Dr. Crenshaw's eyes scanned Alphonse and his brow wrinkled in a sort of recognition, though the boy knew he'd never met this doctor in his life.

"So you're Alphonse? I've heard about you. You might want to hang back a bit. What you see may come as a shock, for both of you."

At this, Roy's stomach clenched. Just what sort of shape was this person in, regardless if it was Edward? Images of the golden haired boy swirled in his mind, covered in gashes, bruised, beaten within an inch of his life, and he gulped down air. He may seem like a hard-ass in the office, but he still thought of the Elric brothers as his own boys, kids he needed to protect. And if Edward was hurt so much as to have some doctor call him down, then warn him of what may lay in that hospital bed… He'd failed. Alphonse swallowed hard before shaking his head.

"No. I'll go in with Colonel Mustang if it's all the same."

Dr. Crenshaw looked between the two again, giving them a moment to prepare, before indicating which room to enter, chart in hand. Roy squeezed Alphonse's shoulder, tightening his grip and the two of them drew a deep breath before walking over to the door. Roy raised a gloved hand to press to the smooth oak door, pausing in hesitation before frowning and pushing it open, guiding Alphonse in the doctor following. What met his eyes was certainly not what he had been expecting.

There was no way the person laying in the bed was Edward Elric, the Fullmetal Alchemist. This person was so breakable looking, fine-boned with soft features and it takes a moment before Roy realizes that this is a girl. A girl with the most obviously feminine attributes he has ever seen and he thinks that maybe the doctor has given him the wrong room. The girl has blond hair, yes, but not Edward's hair. Edward was small, but not this small. Everything about this person screamed 'not Edward' and despite the fact that Roy is about to turn away and walk out to find another room, Alphonse steps forward.

"B-brother?"

Eyes blink open and turn to the sound of Al's voice and even Roy has to stop. Gold. The one feature that is exactly Edward, and so rare in itself that Roy actually sways on his feet when he sees them. Gods, it really may be Edward after all. What the hell had happened? The girl smiles and sits up in bed, holding her arms, both flesh and blood he barely notices, out wide and practically bouncing with excitement.

"Al! You're okay! I was worried when I woke up, I thought that the transmutation hadn't worked!"

Roy almost forgets himself and rounds on Alphonse, about to ask about this transmutation that he'd neglected to mention when he notices the expression on the boy's face. Brow knit and lips drawn tight, Alphonse stays rooted to the spot despite the girl's invitation to come closer. There had to be some mistake. His brother had to be another room.

The girl's smile fades and she glances down at herself before paling. Pulling her arms back in, she tucks them across her bust, wincing and drawing her knees up tight. Roy clears his throat and walks over to the side of the bed. It is then the girl seems to notice him and flushes red, staring up at him through narrowed eyes. Clenching and unclenching his fists, Roy places his hands on the girl's shoulders, wincing at how small and delicate they seem. He came to identify someone as Edward, and he'd do it. Lowering his gaze so that it met gold pools –Edward!- he slowly drew a deep breath before asking in a low, stern tone.

"What did I say to you the first day we met?"

Blinking, the girl's lips twitch up into a grin and Roy can't help but feel that he has seen that expression before. Eyes filled with determination… It is almost as if she is not reciting the words but rather reliving the circumstances surrounding them. In a feminine tenor, the girl speaks words that thrust him back seven years.

"You told me I had a choice. Either live with hopelessness and an empty shell for a brother, or sell myself to the military for the possibility to recover."

Onyx eyes widen and he knows beyond a doubt that the fragile girl before him is in fact Edward Elric. Confusion makes him shake his head and gold eyes dull slightly as Alphonse whimpers behind them. Roy glances over his shoulder at the boy to find that he is battling between sorrow, rage and confusion, and he can empathize. The doctor clears his throat and the three of them jump, having forgotten he was even there.

"It is Edward, there's no doubt about it. At first I didn't believe either, and that led to quite an interesting battle…"

At this Edward's expression darkens and Dr. Crenshaw flinches as though remembering a blow he'd received. Roy glances back at him –or is it her now?- and gives a small chuckle of amusement. The doctor continues.

"A girl, no automail, we had her as a Jane Doe for a while. It wasn't until I saw this that I realized something wasn't quite right."

Dr. Crenshaw reached into his pocket and pulled out Edward's State Alchemist watch, the silver turning and catching the light. Taking the timepiece, Roy scanned the crest before flipping it over to the back, the inscription 'Fullmetal Alchemist' glittering back at him. Nodding, he handed it back to Edward, who clenched it tightly in a fist. Dr. Crenshaw continued, flipping open the heavy looking chart.

"We drew some blood and compared it to past medical history. What we found is interesting to say the least. Now, you may want to sit down for this, it does get quite lengthy."

Roy quirked an eyebrow, then glanced around, grabbing a nearby chair and pulling it closer to the bed. Edward drew the blanket around slim shoulders and sat cross-legged on the bed, eyes fixed to the floor. Alphonse refused to budge, expression now angry more than anything. Flipping to the page he wanted, Dr. Crenshaw found the proper passage and cleared his throat.

"'Case 5583 Edward Elric, blood sample shows genetic anomalies specific to both primary and secondary sexual characteristics. While previous blood tests have shown patient to have XY chromosomes, present blood test shows XX chromosomes present. Previous tests also indicated patient to be within normal hormone range for a sixteen year old male. Present test shows patient to have abnormally high levels of oestrogen, progesterone. Patient exhibits abnormally low levels of testosterone. LH and FSH levels are extremely high-'"

"Whoa, hold on, wait a minute."

Dr. Crenshaw stopped reading and looked up at Roy, who was now rubbing his temples as he attempted to wrap his head around what was being read to him. Edward continued to stare at the floor, face flushing red and fists clenching the blanket. Glancing at the blond, Roy shook his head as he stood, indicating back to the doctor as he took a step towards the bed.

"What the hell does all that mean? What's going on with him?"

Dr. Crenshaw flinched and flipped the chart closed, pushing his glasses back up his nose and sighing. Shifting his weight from one foot to the other, he held out his hands.

"That's just it. Edward isn't showing any male physiology and the blood work keeps coming back as female. I don't know how or why, but Edward is a girl, right down to the genetics."

Roy stood dumbfounded. Of course he had seen physically that Edward was female but… right down to the genes? He looked over at the blond, who seemed to make 'herself' smaller under his stare, and shook his head once more. He wasn't completely up to date on his biology, but he was pretty sure that if someone was born of a specific sex, they didn't just randomly change, at least not without months of therapy and surgeries. Alphonse stared at his brother, brow knit and frowning. After a moment, he turned and walked out the door, Edward tucking further into the blanket, the feeling of having her little brother leave her now like a sting in her heart. Dr. Crenshaw cleared his throat.

"Unfortunately, Edward's hormones are also as if she's going through puberty at breakneck speed. LH and FSH are the hormones that control the development of female physiology and help with production of oestrogen and progesterone. These levels wouldn't be this high in someone who was naturally female at this stage. And while females usually have some testosterone, Edward's is abnormally low, almost non-existent, which leads me to another point."

Roy and Edward both look up at this point, neither knowing what more could have possibly changed. Dr. Crenshaw opens the chart and once again flips to another page. Glancing back up at the members of the room, he decided that it would be best to paraphrase.

"Edward has heightened female characteristics because of the low testosterone: Softer skin, thinner frame, wider hips, thicker hair… Some other genetic characteristics have changed as well, she's now O negative rather than AB. Skin and hair are lighter, obviously. It's odd, she's genetically a blank slate."

That caught Edward's attention and for a moment the Truth's words rang in her ears. Baseline. Blinking, she looked licked her lips before stuttering out.

"'B-blank slate?' Doc, I'd heard somewhere that females were a genetic baseline. Is that what you mean?"

Dr. Crenshaw stared back at her for a moment, then snickered at the thought. Roy stared curiously at Edward, who simply ignored him in favour of the doctor. Nodding his head, Dr. Crenshaw raised his arms across his chest, one hand on his chin as the meaning of the words sank in. After a moment, he returned his attention to the two.

"That's a brilliant way of putting it. You see, everyone starts out female in the womb, then is changed within the first month to the sex determined by their genes, which determine hormone output. Females can only carry the X chromosome because that is the only one they have, therefore the males determine the sex of offspring. Even if a male embryo doesn't receive the proper level of hormones indicated by their genetics, the fetus develops primarily as female. It's nature's default setting."

Edward shivered at the thought. Right down to genetic makeup, the Truth really did have the baseline it wanted. It was frightening. It was infuriating. Edward wanted to vomit at the thought. No, hit something! The Truth had never made it clear what 'conditions' it had meant. Now Edward had no control of his, no her body and she felt tears sting her eyes. The doctor turned back to Roy, who had grown considerably pale and quiet in all this, and continued on.

"Edward's body is going to change very rapidly in the next few weeks. She may grow breasts, she may even menstruate, and she will be in pain. It won't be easy for her-"

"'Him!'"

Two pairs of wide eyes spun to Edward, who was now glaring back at the doctor with tears streaking down flushed cheeks. Standing, Edward threw the blanket off, shaking as she stepped forward, fists clenched around the pocket watch and eyes narrowed dangerously. Catching her breath, she growled.

"'Him!' I'm still a guy! I'm still Edward! I like poker and sports and alchemy and sparring! I'm not a girl, I don't want this body! I don't know why the Truth put me in it but I'm still a guy!"

Hot frustration filled her and she shook at the need to release it. Her eyes clenched shut and her teeth grit, she squared her shoulders. Dropping the pocket watch, Edward brought her hands together and reached over, pressing her left to the wall with every intention of breaking some drywall. However, when the skin of her hand connected with the wall, she didn't feel the familiar electricity that came with transmuting. Peaking open her eyes, she turned to find the wall completely unmarked and unchanged,

Fear replaced anger and Edward's jaw dropped as she glanced down at her hands. Gulping, she clapped her hands again, determined that she hadn't been concentrating and merely needed to focus. Hands slapped against the wall again and still nothing happened. Giving as strangled sob, she repeated the process again and again, tears again streaking her face as she ground out a frustrated cry.

"Why isn't it working!"

Roy gaped in shock as he and the doctor watched Edward, his heart sinking and stomach in knots as she continued to try to transmute, hands turning red from the effort. Blinking himself out of his reverie, Roy stepped forward and grabbed Edward around the waist, nearly dropping her as he found she was far lighter now that she was female. Pulling Edward away from the wall, he fought to keep his balance as she struggled to transmute. Groaning as one of Edward's elbows caught him in the ribs, he looked over to Dr. Crenshaw for help, who seemed to want no part I getting involved with a struggling Edward. He ended up thrown off balance and fell ungracefully onto the bed, Edward's back against his chest and he quickly grabbed her wrists to keep her from clapping again.

"Let go, Bastard! I gotta try! I have to be able to transmute! I've only got ten months!"

Grip tightening, Roy frowned at the last few words. Pulling Edward's arms across her chest and pinning them there, he shifted her weight so that she was sitting on the bed next to him, still tucked close so she couldn't wiggle away. After a moment of catching his breath, he looked down at Edward's flushed and tear-streaked face.

"What do you mean you only have ten months?"

Edward stopped struggling and let out another whimper. Soft yellow waves blocked her face and Roy felt her sobs shake her body. Sighing, he loosened his grip, surprised when she didn't jump straight into more transmutations. After a few minutes, Edward spoke in a soft, broken voice.

"Before I turned up like this, I was back inside the Gate. The Truth said that it wasn't happy that we both survived with the price of one. The Truth told me it would give me ten months to pay what's owed for Al's body. If I don't find a way to pay, we both die."

With a sinking feeling in his heart, Roy closed his eyes and pulled the young boy-turned-girl closer to him, wrapping her in a hug. First Edward had been turned into a girl, now she couldn't transmute and one of the worst deadlines imaginable was looming a mere ten months away. Roy was right: Today was not going well.

* * *

><p>I know I said Friday. That's what happens when people at work get sick and you have to cover. If there are any questions about what I wrote, again, google.<p> 


	4. 3: Dysphoria

_baseline (beys-lahyn) – 1. a basic standard or level; guideline. 2. a specific value to establish control in future studies._

**Baseline**

**secondhandsaint**

**3: Dysphoria**

The drive back to CHQ had been a quiet and uncomfortable one to say the least. Alphonse sat in the back seat, staring out the window, body tense and expression bordering sorrow and fury. Edward sat in the front seat, hands clutching a rather thick stack of pamphlets of what to expect in her 'change,' pictures of pretty teenage girls smiling up at her. Like her brother, she stared out the window at the buildings blurring past, though seemed numb to her surroundings. Roy had been glancing between the Elrics, sighing in relief at the sight of the dorm building, parking and guiding the two inside. Thankfully it had been midday by the time Edward had been discharged, so by the time they got to the dorms they were all but deserted, their occupants busy with work in the main building.

Pulling out a set of keys, Roy walked to the dorm room the eldest stayed in, unlocking the door and pushing it open. Edward shoved past him and inside, throwing the pamphlets on the coffee table and running to the bathroom, door slamming behind her. Roy blinked and followed Alphonse inside, who sat on the couch with a huff, eyes on the scattered papers and jaw clenched. Setting the keys down, Roy shrugged off his coat, walking over to the kitchenette and flicking the kettle on to make tea. Glancing over his shoulder at Alphonse, he pulled open the cupboard he hoped held the mugs.

"Al, you want some tea?"

The boy remained silent, hands clenched into fists on his knees as he continued to stare at the pamphlets. Through the bathroom door, the sound of the shower turning on filled the silence and Alphonse flinched slightly, lips a thin line. His eyes were fixed on one particular girl on the cover of one paper, whose face vaguely resembled the one that Edward now wore. Sighing, Roy pulled down three mugs, just in case. He set about busying himself around the kitchen when he heard Alphonse mutter something and looked up, shocked.

"Eh? What was that, Al?"

The boy's head shot up, face red and eyes wide as he fixed his stare on Roy. In turn, Roy backed up a step, never once having seen Alphonse with such an intense look upon his face, and it honestly frightened him. Alphonse shook as he spoke, teeth grit.

"Ed sacrificed himself again! It came to another choice between me or him and he chose himself again! I know it!"

Roy wasn't quite sure what to say at Alphonse's outburst, though he didn't really have a chance to reply. Mug in one hand and teabag in the other, he stared dumbly as the younger Elric took another breath and continued on in his rant.

"I know that everything needed to restore Ed was included in the transmutation, so Truth must have wanted something else from us and Ed stupidly put himself in the crossfire again! Now what are we supposed to do? Am I supposed to start calling him 'Sister'?"

Roy was about to answer when he realized that this was not a completely off-base question. Just what were the Elrics supposed to do now? Sighing, he put the mug and bag down, forgetting about the tea for the moment and sitting in the chair across from Alphonse. After a moment's consideration he nodded and looked up at the boy.

"I think he did what he needed to in order to keep you both alive, but-"

He held up a hand as Alphonse went to interrupt him, eyes stern as the boy begrudged having to obey orders from a man who wasn't even his superior officer. Confident that Alphonse wouldn't interrupt again, Roy continued on.

"There's a whole other part of the story that you don't know about yet."

Alphonse's eyes became wide at this and his jaw dropped slightly. The hazel gaze shifted to the door of the bathroom as if staring through it to the person inside. Swallowing hard at this news, Alphonse furrowed his brow and turned back to Roy, hands flat against his knees to steel himself.

"Tell me everything."

* * *

><p>Edward waited for the water to heat, running his now flesh right hand under the stream and taking just the slightest satisfaction of being able to feel with his dominant hand for once. The joy faded quickly and he clenched his jaw, pulling his hand back and shaking the water off. Slipping his now gaping red coat off, he was about to strip to get into the shower when his slightly fogged reflection caught his eyes.<p>

It felt like he was looking at some poster or into a bad dream. It made fury stir hot in his gut and rather than breaking a mirror and risking seven years bad luck, he improvised. Throwing the coat up and hooking it onto the light fixture above the mirror, the reflection disappeared and the room bathed in red. Nodding at his work, Edward began to strip, careful to look away when he pulled off his tank top and boxers.

Stepping into the hot stream, Edward all but groaned as the hot water pounded against his sore muscles, body tired from reshaping itself. Tilting his head back he wet his hair down, quickly scrubbing the remnants of three days in hospital from the strands. Rinsing the suds, he reached down and picked up the soap from the ledge. Shutting his eyes tight, he began washing his body, teeth clenched as he tried to ignore the swell of his chest, the way the muscles in his shoulders and arms were still toned but so much smaller, his hips seemed shapelier.

Not willing to skip on hygiene, Edward steeled himself before moving one hand down his stomach, hesitating when his fingertips brushed soft yellow curls. It was just anatomy, for crying out loud! He'd seen this in research before. Hell, he'd even enjoyed seeing it in the adult magazines he had shoved in his bedside dresser. But looking at a naked girl and being one were two very different things.

Edward blinked his eyes open and fixed his stare at the blue tiles across from him. He knew if he hesitated and didn't just get it over with, it would be much worse. He could do this. Biting his lip, he pushed onward. With his body so newly developed, it hurt to touch and the soap wasn't helping. Hissing, he quickly pulled his hand away. Once the sting and sore ache dulled away he continued, glancing down. His male mind immediately registered what was lacking in this female body and despite himself he choked. This wasn't the right anatomy. This wasn't the right body!

Bile pushed up his throat and Edward barely had the time to jump out of the shower and run to the toilet before he heaved. Coughing and spitting, Edward wiped his mouth before stepping back and sitting on the edge of the bathtub. Clenching his eyes shut, he sighed at his own behavior. It was selfish, and he didn't have time for selfish. Al didn't have time for selfish. He would just have to learn to deal. He had to get used to the body, even if it was just as simple as bathing and learning to work in it. He was going to be stuck in it for another ten months, after all.

Opening his eyes, he clenched his jaw, hands pressed again to his lower stomach. It was just anatomy. Repeating it in his head like a mantra, he stepped back into the shower to rinse the soap from his body. Water off, he stepped out, towel drying his hair and rummaging through the hamper in the corner for the baggiest t-shirt and sweatpants he owned.

* * *

><p>Roy and Alphonse both looked up when the bathroom door opened, Edward walking out with a pile of clothes in her arms. Two pairs of eyes watched her as she padded over to the bed in the corner, scanning the pajamas that dwarfed her and the wet hair hanging to her butt. Glancing at each other, the two stared as Edward dropped her clothes onto the bed, pulling on a sweater and walking over to the coffee table. Grabbing the pile of scattered pamphlets, Edward walked into the kitchenette, opened the cupboard under the sink and tossed the papers into the trash. Without pause, she stood straight and collected her tea, padding back into the living room to see both staring at her.<p>

"What?"

Roy tapped his fingers on the back of the sofa, wondering briefly how to say what he was about to without causing Edward to fly off the handle. He realized that there really wasn't a delicate way of saying it, so he just did.

"Don't you think it's wise to keep those pamphlets around? You're going to need them to learn about some… feminine issues?"

Edward quirked a delicate brow and stared at him from where she stopped dead at his statement. Shaking it off she sat down next to Al, not at all daintily, and blew on her tea.

"Winry was never shy when it came to sharing about periods and bra sizes. I think I'm caught up."

Roy certainly hadn't been expecting that. He had always figured that the two friends were extremely close, but that they shared that type of intimate information was astounding. Noting the slight blush Edward was trying to hide behind the rim of her mug, Roy decided to drop the issue, though made a mental note to fish the pamphlets out of the trash before he left.

An uncomfortable silence filled the room as the three sat, deciding how to go about discussing the elephant in the room. Roy stared between the brothers (brother and sister?), while they would occasionally glance at each other when they knew they weren't looking. The tension grew and it set Roy's teeth on edge, making him want to shout at the Elrics to just say something. Fidgeting in her seat, Edward finally put her mug down, rubbing her sweaty palms on her knees before turning to her little brother.

"Al… I gotta tell you something about while I was gone. I… I was in the Gate again, Al, and I saw Truth."

Al stiffened, back straight and fists clenched, eyes firmly set on floor. Fear, anger and sadness rolled off of him in waves and it made Edward want to shy away. She hated hurting her brother, making him worry, and she wanted desperately to tell him 'never mind,' that she'd deal with it. But she couldn't keep him in the dark about her mistake when the cost was so high. Glancing as Roy, who nodded, Edward took a breath.

"Al, Truth wants me to finish the payment-"

'For my body, I know."

Blinking, Edward drew back a moment before rounding on Roy, glaring as though he had claimed 'witch' on her.

"You ass!"

Roy held up his hands and slid further into the cushions. Al jumped to his rescue.

"Brother!"

Hearing Al address her as male made just the tiniest flutter of relief and pride swell in Edward's stomach, which was quickly squashed by his scowl. Of all the things Al had learned over the years travelling together with his brother, unfortunately Edward's temper was one.

"Colonel Mustang told me because I asked him to! Now I know that you picked yourself over me to bear the brunt of our stupidity! And that you're female down to the genetic makeup! And that if we don't figure out a way of paying back for my body, we both die! I don't know how the hell we're supposed to do this in ten months, with you a tiny girl and stripped of alchemy!"

Edward had cowered away from his little brother during his rant, eyes downcast and hands fisted in his lap. Roy watched as Al fumed, shoulders rising and falling at the intensity of his breaths, eyes staring at the blonde beside him. Al raised his hands and for a moment he thought that the younger Elric would strike her, but was again surprised as his arms wrapped around Edward, pulling her tight against his chest.

"I'm glad you're alive."

Edward's eyes widened a moment before closing and hugging her brother. Roy nodded, standing and placing his mug in the sink. Pulling his jacket on, he watched as the two parted and began discussing the task at hand, knowing that for the time being they would be alright.

* * *

><p>I'm sorry for the late update. Not much going on in this chapter, but the part with Edward in the bathroom is very important. Whenever Edward isn't alone, he is referred to as 'she.' When alone, Edward is a he, as that is what Edward identifies as. This will continue through the fiction.<p> 


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